MolNFT v1 · #164951 · protein
Crystal structure of a galactokinase from bifidobacterium infantis in complex with ADP
6TEP: “Crystal structure of a galactokinase from bifidobacterium infantis in complex with ADP”. X-ray diffraction, 3 ligands (ADP, MG, CL), 15 pockets (best druggability 0.78). MolNFT v1 #164951 on GenesisL1: 3D structure, binding sites…
- PDB
- 6TEP
- Type
- protein
- Length
- 1,658 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Galactokinase
- UniProt
- B7GUI0
- Ligands
- ADP, MG, CL
- Pockets
- 15 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 44% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Galactokinase | protein | 414 | 45% helix, 21% strand | B7GUI0 |
| D | Galactokinase | protein | 413 | 43% helix, 20% strand | B7GUI0 |
| C | Galactokinase | protein | 415 | 45% helix, 20% strand | B7GUI0 |
| B | Galactokinase | protein | 416 | 44% helix, 20% strand | B7GUI0 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 4 copies · chains A, D, C, B
- MG · Magnesium ion · metal · 4 copies · chains A, D, C, B
- CL · Chloride ion · ion · 5 copies · chains A, D, C, B
- PEG · Di(hydroxyethyl)ether · additive · 11 copies · chains A, D, C, B
- GOL · Glycerol · additive · 9 copies · chains A, C, D, B
- PG4 · Tetraethylene glycol · additive · chains C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1006 | 0.78 | 0.80 | 84 | PEG, GOL, ADP, MG |
| 2 | 716 | 0.73 | 0.79 | 78 | empty |
| 3 | 469 | 0.69 | 0.80 | 49 | GOL, ADP, MG |
| 4 | 410 | 0.66 | 0.79 | 53 | PEG, GOL, ADP, MG |
| 5 | 388 | 0.64 | 0.79 | 52 | GOL, ADP, MG |
Interfaces
3 interfaces between chains.
- C–B · 365 Ų buried · 4 hydrogen bonds · protein-protein
- A–C · 286 Ų buried · 2 hydrogen bonds · protein-protein
- D–B · 193 Ų buried · 1 hydrogen bond · protein-protein
Compared structures
- 6TEP · Crystal structure of a galactokinase from Bifidobacterium infantis in complex with ADP · the same entry in another collection · chain B against B, TM-score 1.00
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt B7GUI0
- Elsewhere: RCSB PDB 6TEP · PDBe 6TEP · UniProt B7GUI0
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